add hifiasm-meta 0.3.5

Program_Licenses.md

@@ -83,6 +83,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Gubbins | GNU GPLv2 | https://github.com/nickjcroucher/gubbins/blob/master/LICENSE |
 | HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE ; https://github.com/erinyoung/heatcluster/blob/main/LICENSE |
 | Hifiasm | MIT | https://github.com/chhylp123/hifiasm/blob/master/LICENSE |
+| hifiasm-meta | MIT | https://github.com/xfengnefx/hifiasm-meta/blob/meta/LICENSE |
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
 | HoCoRT | MIT | https://github.com/ignasrum/hocort?tab=MIT-1-ov-file#readme |
 | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |

README.md

@@ -190,7 +190,8 @@ To learn more about the docker pull rate limits and the open source software pro
 | [grandeur_ref](https://hub.docker.com/r/staphb/grandeur_ref) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/grandeur_ref)](https://hub.docker.com/r/staphb/grandeur_ref) | <details><summary>Click to see all versions</summary> <ul><li>[4.5](./build-files/grandeur_ref/4.5/)</li><li>[4.6](./build-files/grandeur_ref/4.6/)</li></ul> </details> | Part of https://github.com/UPHL-BioNGS/Grandeur |
 | [Gubbins](https://hub.docker.com/r/staphb/gubbins) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gubbins)](https://hub.docker.com/r/staphb/gubbins) | <details><summary>Click to see all versions</summary> <ul><li>[3.3.3](./build-files/gubbins/3.3.3/)</li><li>[3.3.4](./build-files/gubbins/3.3.4/)</li><li>[3.3.5](./build-files/gubbins/3.3.5/)</li><li>[3.4.1](./build-files/gubbins/3.4.1/)</li></ul> </details> | https://github.com/nickjcroucher/gubbins |
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.2c](./build-files/heatcluster/1.0.2c/)</li><li>[1.3.0](./build-files/heatcluster/1.3.0/)</li></ul> </details> | https://github.com/DrB-S/heatcluster/tree/main ; https://github.com/erinyoung/heatcluster/tree/main |
-| [hifiasm](https://hub.docker.com/r/staphb/hifiasm) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hifiasm)](https://hub.docker.com/r/staphb/hifiasm) | <details><summary>Click to see all versions</summary> <ul><li>[0.25.0](./build-files/heatcluster/0.25.0/)</li></ul> </details> | https://github.com/chhylp123/hifiasm/tree/master |
+| [hifiasm](https://hub.docker.com/r/staphb/hifiasm) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hifiasm)](https://hub.docker.com/r/staphb/hifiasm) | <details><summary>Click to see all versions</summary> <ul><li>[0.25.0](./build-files/hifiasm/0.25.0/)</li></ul> </details> | https://github.com/chhylp123/hifiasm |
+| [hifiasm-meta](https://hub.docker.com/r/staphb/hifiasm-meta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hifiasm-meta)](https://hub.docker.com/r/staphb/hifiasm-meta) | <details><summary>Click to see all versions</summary> <ul><li>[0.3.5](./build-files/hifiasm-meta/0.3.5/)</li></ul> </details> | https://github.com/xfengnefx/hifiasm-meta |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <details><summary>Click to see all versions</summary> <ul><li>[3.3](./build-files/hmmer/3.3/)</li><li>[3.3.2](./build-files/hmmer/3.3.2/)</li><li>[3.4](./build-files/hmmer/3.4/)</li></ul> </details> | http://hmmer.org/ |
 | [hocort](https://hub.docker.com/r/staphb/hocort) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hocort)](https://hub.docker.com/r/staphb/hocort) | <details><summary>Click to see all versions</summary> <ul><li>[1.2.2](./build-files/hocort/1.2.2/)</li></ul> </details> | https://github.com/ignasrum/hocort |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <details><summary>Click to see all versions</summary> <ul><li>[0.4.1](./build-files/homopolish/0.4.1/)</li></ul> </details> | https://github.com/ythuang0522/homopolish/ |

build-files/hifiasm-meta/0.3.5/Dockerfile

@@ -0,0 +1,52 @@
+ARG HIFIASM_META_VER="0.3.5"
+
+## Builder ##
+FROM ubuntu:noble AS builder
+
+ARG HIFIASM_META_VER
+
+RUN apt-get update && apt-get install -y \
+    wget \
+    build-essential \
+    zlib1g-dev &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# hifiasm-meta
+RUN wget https://github.com/xfengnefx/hifiasm-meta/archive/refs/tags/hamtv${HIFIASM_META_VER}.tar.gz &&\
+    tar -xvf hamtv${HIFIASM_META_VER}.tar.gz && rm hamtv${HIFIASM_META_VER}.tar.gz &&\
+    cd hifiasm-meta-hamtv${HIFIASM_META_VER} && make &&\
+    mv hifiasm_meta /usr/local/bin/
+
+## App ##
+FROM ubuntu:noble AS app
+
+ARG HIFIASM_META_VER
+
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="hifiasm-meta"
+LABEL software.version="${HIFIASM_META_VER}"
+LABEL description="A hifiasm fork for metagenome assembly using Hifi reads"
+LABEL website="https://github.com/xfengnefx/hifiasm-meta"
+LABEL license="https://github.com/xfengnefx/hifiasm-meta/blob/meta/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+COPY --from=builder /usr/local/bin/hifiasm_meta /usr/local/bin/
+
+ENV LC_ALL=C
+
+CMD ["hifiasm_meta"]
+
+WORKDIR /data
+
+## Test ##
+FROM app AS test
+
+RUN hifiasm_meta -h
+
+# test hifiasm-meta (requires ~18GB of RAM.)
+# RUN apt-get update && apt-get install -y wget
+# RUN wget -q https://zenodo.org/records/5908204/files/zymoD6331std-ecoli-ten-percent.fq.gz?download=1 -O test.fq.gz &&\
+#     hifiasm_meta -t4 --force-rs -o asm test.fq.gz 2>asm.log
+

build-files/hifiasm-meta/0.3.5/README.md

@@ -0,0 +1,30 @@
+# hifiasm-meta container
+
+Main tool: [hifiasm-meta](https://github.com/xfengnefx/hifiasm-meta/)
+
+Code repository: https://github.com/xfengnefx/hifiasm-meta
+
+Additional tools:
+- none
+
+Basic information on how to use this tool:
+- executable: `hifiasm_meta`
+- help: `-h`
+- version: `--version`
+- description: A hifiasm fork for metagenome assembly using Hifi reads.
+
+Additional information:
+
+Feng, X., Cheng, H., Portik, D., & Li, H. (2022). Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods, 19(6), 671–674. https://doi.org/10.1038/s41592-022-01478-3
+
+‌  
+Full documentation: https://github.com/xfengnefx/hifiasm-meta
+
+## Example Usage
+
+```bash
+hifiasm_meta -t32 -o asm reads.fq.gz 2>asm.log
+
+# if the dataset has high redundancy
+hifiasm_meta -t32 --force-rs -o asm reads.fq.gz 2>asm.log  
+```